According to the New York City Police Department, two of the boys are 14 years old, one is 12 and the fourth is 11.
They were arrested Thursday, and charged as juveniles with arson and criminal mischief as a hate crime.
An 11-year-old boy already was charged in connection with the Sunday evening blaze.
Police say surveillance video showed a group of boys running off the bus as it catches on fire.
The bus belonged to the Bnos Chomesh Academy, a girls' high school in Brooklyn's Crown Heights. It's a neighborhood where tensions between the Jewish and black communities living side by side spurred riots in 1991.
The investigation is continuing.
The NYPD also released surveillance video from the scene of the fire.
As many as five boys were on the parked bus when the boy lit the fire just after 6 p.m. Sunday night outside a Jewish elementary school on Lefferts Avenue in the Crown Heights section, police say.